dbSNP rs2641670: CRISPLD2:c.*732G>A (chr16-84907374-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031476.4(CRISPLD2):c.*732G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,412 control chromosomes in the GnomAD database, including 5,302 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 5297 hom., cov: 33)

Exomes 𝑓: 0.18 ( 5 hom. )

Consequence

CRISPLD2
NM_031476.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.477

Publications

8 publications found

Variant links:

Genes affected

CRISPLD2 (HGNC:25248): (cysteine rich secretory protein LCCL domain containing 2) Predicted to enable glycosaminoglycan binding activity. Involved in face morphogenesis. Located in transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

CRISPLD2 links:

ENSG00000279622 (HGNC:):

ENSG00000279622 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031476.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD2	NM_031476.4	MANE Select	c.*732G>A		3_prime_UTR	Exon 15 of 15	NP_113664.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CRISPLD2	ENST00000262424.10	TSL:1 MANE Select	c.*732G>A	3_prime_UTR	Exon 15 of 15	ENSP00000262424.5
CRISPLD2	ENST00000566165.1	TSL:3	n.120-12266G>A	intron	N/A	ENSP00000463171.1
ENSG00000279622	ENST00000741212.1		n.221+16169C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39355

AN:

152032

Hom.:

5281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.292

GnomAD4 exome

AF:

0.179

AC:

AN:

262

Hom.:

Cov.:

AF XY:

0.189

AC XY:

AN XY:

206

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.375

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.180

AC:

AN:

222

Other (OTH)

AF:

0.0714

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.259

AC:

39409

AN:

152150

Hom.:

5297

Cov.:

AF XY:

0.261

AC XY:

19378

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.287

AC:

11919

AN:

41506

American (AMR)

AF:

0.338

AC:

5169

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.240

AC:

833

AN:

3468

East Asian (EAS)

AF:

0.288

AC:

1485

AN:

5162

South Asian (SAS)

AF:

0.240

AC:

1161

AN:

4828

European-Finnish (FIN)

AF:

0.211

AC:

2233

AN:

10586

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.229

AC:

15595

AN:

67996

Other (OTH)

AF:

0.289

AC:

611

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1517

3033

4550

6066

7583

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.236

Hom.:

3931

Bravo

AF:

0.269

Asia WGS

AF:

0.256

AC:

890

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.8

(source)

DANN

Benign

0.54

PhyloP100

-0.48

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over